libsecret credentials

.bashrc.kuba

@@ -43,7 +43,7 @@ source_existing ~/.bash_prompt.kuba
 source_existing ~/.python-venv.kuba/bin/activate
 
 if command -v ipython &> /dev/null; then
-    alias p=ipython
+    alias p="ipython --pylab"
 elif command -v python &> /dev/null; then
     alias p=python
 fi

.config/okularpartrc

@@ -1,12 +0,0 @@
-[$Version]
-update_info=okular.upd:annotation-toolbar,okular.upd:builtin-annotations
-
-[Identity]
-IdentityAuthor=Jakub Fojt
-
-[Main View]
-SplitterSizes=145,719
-
-[Reviews]
-BuiltinAnnotationTools=<tool name="Yellow Highlighter" type="highlight" id="1"><engine type="TextSelector" color="#fff9f06b"><annotation type="Highlight" opacity="0.5" color="#fff9f06b"/></engine><shortcut>2</shortcut></tool>,<tool type="underline" id="2"><engine type="TextSelector" color="#ff0000"><annotation type="Underline" color="#ffff0000"/></engine></tool>,<tool type="squiggly" id="3"><engine type="TextSelector" color="#ff0000"><annotation type="Squiggly" color="#ffff0000"/></engine></tool>,<tool type="strikeout" id="4"><engine type="TextSelector" color="#ff0000"><annotation type="StrikeOut" color="#ffff0000"/></engine></tool>,<tool name="Totalpoäng" type="typewriter" id="5"><engine type="PickPoint" block="true"><annotation textColor="#1a5fb4" type="Typewriter" color="#00ffffff" width="0" font="Cantarell\\,26\\,-1\\,5\\,50\\,0\\,0\\,0\\,0\\,0"/></engine></tool>,<tool type="note-inline" id="6"><engine hoverIcon="tool-note-inline" type="PickPoint" block="true" color="#ffff00"><annotation textColor="#ff000000" type="FreeText" color="#ffffff00"/></engine></tool>,<tool name="Yellow popup note" type="note-linked" id="7"><engine hoverIcon="tool-note" type="PickPoint" color="#fff9f06b"><annotation icon="Comment" type="Text" color="#fff9f06b"/></engine><shortcut>8</shortcut></tool>,<tool type="ink" id="8"><engine type="SmoothLine" color="#00ff00"><annotation type="Ink" color="#ff00ff00" width="2"/></engine></tool>,<tool name="Arrow" type="straight-line" id="9"><engine type="PolyLine" color="#000000" points="2"><annotation type="Line" endStyle="3" color="#ff000000" width="2"/></engine></tool>,<tool type="straight-line" id="10"><engine type="PolyLine" color="#000000" points="2"><annotation type="Line" color="#ff000000" width="2"/></engine></tool>,<tool name="Yellow transparent fill" type="rectangle" id="11"><engine type="PickPoint" block="true" color="#fff9f06b"><annotation type="GeomSquare" opacity="0.5" color="#fff9f06b" innerColor="#f9f06b" width="5"/></engine><shortcut>5</shortcut></tool>,<tool name="Green transparent fill" type="ellipse" id="12"><engine type="PickPoint" block="true" color="#ff33d17a"><annotation type="GeomCircle" opacity="0.5" color="#ff33d17a" innerColor="#33d17a" width="5"/></engine><shortcut>6</shortcut></tool>,<tool type="polygon" id="13"><engine type="PolyLine" color="#007eee" points="-1"><annotation type="Line" color="#ff007eee" width="2"/></engine></tool>,<tool type="stamp" id="14"><engine hoverIcon="Sold" type="PickPoint" block="true" size="64"><annotation icon="Sold" type="Stamp"/></engine></tool>
-QuickAnnotationTools=<tool id="1" name="Red highlighter" type="highlight"><engine type="TextSelector" color="#fff66151"><annotation opacity="0.5" type="Highlight" color="#fff66151"/></engine><shortcut>1</shortcut></tool>,<tool id="2" name="Yellow Highlighter" type="highlight"><engine type="TextSelector" color="#fff9f06b"><annotation opacity="0.5" type="Highlight" color="#fff9f06b"/></engine><shortcut>2</shortcut></tool>,<tool id="3" name="Green Highlighter" type="highlight"><engine type="TextSelector" color="#ff8ff0a4"><annotation opacity="0.5" type="Highlight" color="#ff8ff0a4"/></engine><shortcut>3</shortcut></tool>,<tool id="4" name="Red transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#fff66151"><annotation width="5" innerColor="#f66151" opacity="0.5" type="GeomSquare" color="#fff66151"/></engine><shortcut>4</shortcut></tool>,<tool id="5" name="Yellow transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#fff9f06b"><annotation width="5" innerColor="#f9f06b" opacity="0.5" type="GeomSquare" color="#fff9f06b"/></engine><shortcut>5</shortcut></tool>,<tool id="6" name="Green transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#ff8ff0a4"><annotation width="5" innerColor="#8ff0a4" opacity="0.5" type="GeomSquare" color="#ff8ff0a4"/></engine><shortcut>6</shortcut></tool>,<tool id="7" name="Red popup note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#fff66151"><annotation icon="Comment" type="Text" color="#fff66151"/></engine><shortcut>7</shortcut></tool>,<tool id="8" name="Yellow popup note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#fff9f06b"><annotation icon="Comment" type="Text" color="#fff9f06b"/></engine><shortcut>8</shortcut></tool>,<tool id="9" name="Green pop-up note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#ff8ff0a4"><annotation icon="Comment" type="Text" color="#ff8ff0a4"/></engine><shortcut>9</shortcut></tool>,<tool id="10" type="note-inline"><engine hoverIcon="tool-note-inline" block="true" type="PickPoint" color="#ffff00"><annotation textColor="#ff000000" type="FreeText" color="#ffffff00"/></engine></tool>,<tool id="11" name="Insert Text" type="typewriter"><engine block="true" type="PickPoint"><annotation width="0" textColor="#000000" type="Typewriter" color="#00ffffff"/></engine></tool>,<tool id="12" name="Totalpoäng" type="typewriter"><engine block="true" type="PickPoint"><annotation width="0" textColor="#1a5fb4" type="Typewriter" font="Cantarell\\,26\\,-1\\,5\\,50\\,0\\,0\\,0\\,0\\,0" color="#00ffffff"/></engine></tool>,<tool id="13" type="underline"><engine type="TextSelector" color="#ff0000"><annotation type="Underline" color="#ffff0000"/></engine></tool>

.config/picom.conf

@@ -121,7 +121,12 @@ inactive-opacity-override = false;
 
 # Specify a list of conditions of windows that should never be considered focused.
 # focus-exclude = []
-focus-exclude = [ "class_g = 'Cairo-clock'" ];
+focus-exclude = [ "class_g = 'Cairo-clock'",
+                  "class_g = 'firefox'",
+                  "class_g = 'zoom'",
+                  "class_g = 'Soffice'",
+                  "class_g = 'libreoffice-impress'"
+                ];
 
 # Use fixed inactive dim value, instead of adjusting according to window opacity.
 # inactive-dim-fixed = 1.0

.gitconfig

@@ -7,7 +7,7 @@
 	process = git-lfs filter-process
 	required = true
 [credential]
-	helper = cache --timeout=3600
+	helper = libsecret
 [color]
 	ui = auto
 [pull]

.i3initrc

@@ -5,18 +5,18 @@
 i3config="/tmp/i3_${USER}_config"
 rm -f $i3config
 
-if [ -f ~/.i3/base.config ]; then
+if [ -f "$HOME/.i3/base.config" ]; then
-    cat ~/.i3/base.config >> $i3config
+    cat "$HOME/.i3/base.config" >> $i3config
 fi
 
-if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f ~/.i3/home.config ]; then
+if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f "$HOME/.i3/home.config" ]; then
-    cat ~/.i3/home.config >> $i3config
+    cat "$HOME/.i3/home.config" >> $i3config
-elif [ "`hostname`" = "kubaDesktop" ] && [ -f ~/.i3/home.config ]; then
+elif [ "`hostname`" = "kubaDesktop" ] && [ -f "$HOME/.i3/home.config" ]; then
-    cat ~/.i3/home.config >> $i3config
+    cat "$HOME/.i3/home.config" >> $i3config
-elif [ "`hostname`" = "JakubArch" ] && [ -f ~/.i3/work.config ]; then
+elif [ "`hostname`" = "JakubArch" ] && [ -f "$HOME/.i3/work.config" ]; then
-    cat ~/.i3/work.config >> $i3config
+    cat "$HOME/.i3/work.config" >> $i3config
 fi
 
 #exec i3 -c $i3config -V >> ~/${WM}.log 2>&1
-sh ~/.i3/scripts/displays.sh auto
+sh "$HOME/.i3/scripts/displays.sh" auto
 exec i3 -c $i3config

.modules.kuba/.tools.sh

@@ -11,12 +11,18 @@ except ImportError:
 class Wrap:
     def __init__(self, fname):
         n = np.load(fname, allow_pickle=True)
-        files = n.files
         globs = globals()
-        print('Contains files', files)
+        if isinstance(n, np.lib.npyio.NpzFile):
-        for f in files:
+            files = n.files
-            setattr(self, f, n[f])
+            print('Contains files', files)
-            globs[f] = n[f]
+            for f in files:
+                setattr(self, f, n[f])
+                globs[f] = n[f]
+        else:
+            print('Loaded data of shape', n.shape)
+            setattr(self, 'data', n)
+            globs['data'] = n
+
 
 argv = argv[argv.index('--')+1:]
 archives = [Wrap(arg) for arg in argv]
@@ -94,3 +100,32 @@ watch_modify() {
         [ "$base" == "$file_name" ] && echo ${@:2} && ${@:2}
     done
 }
+
+pdftoclipboard() {
+    if [ $# -lt 1 ]; then
+        echo "Usage pdftoclipboard FILE [DPI]
+
+        Convert pdf file FILE to png and copy to clipboard. Default DPI is 600
+        "
+        return
+    fi
+    file="$1"
+    dpi="${2:-600}"
+
+    pdftoppm -png -r "$dpi" "$file"  | xclip -sel clip -t image/png -i
+}
+
+gitgrepsed() {
+    if [ $# -lt 2 ]; then
+        echo "Usage gitgrepsed SEARCH REPLACE
+
+Search and replace in git repository.
+Alias for git grep -l \$SEARCH | xargs sed -i "s/\$SEARCH/\$REPLACE/g"
+        "
+        return
+    fi
+
+    search="$1"
+    replace="$2"
+    git grep -l "$search" | xargs sed -i "s/$search/$replace/g"
+}

.modules.kuba/node.lua

@@ -0,0 +1,3 @@
+local home = os.getenv("HOME")
+local pkg  = pathJoin(home, "node-v21.1.0-linux-x64")
+prepend_path("PATH", pathJoin(pkg, "bin"))

.modules.kuba/slurm-aliases.lua

@@ -3,9 +3,11 @@ Defines useful SLURM aliases
 ]==])
 
 set_alias("si", 'sinfo -e -o "%9P %4a %8s %.10l %11A %6z %.7m %40N"')
-set_alias("q",  'squeue -u $USER -o "%7A %56j %2t %16S %.10M %.10L %.2D %4N"')
+set_alias("q",  'squeue -u $USER -o "%8A %56j %2t %16S %.10M %.10L %.2D %4N"')
 set_alias("ql", 'squeue -u $USER -o "%8A %7K %56j %2t %3r %16S %.10M %.10L %.4D %8N %4f"')
+set_alias("qll", 'squeue -u $USER -o "%8A %7K %150j %2t %3r %16S %.10M %.10L %.4D %8N %4f"')
 set_alias("qa", 'squeue -o "%8A %10u %.6Q %24j %2t %3r %16S %.10M %.10L %.4D %16N" -S t,-p | less')
+set_alias("qq", 'squeue -u $USER -o "%8A %7K %76j %9F %2t %.10L"')
 set_alias("qid", 'squeue -h -u $USER -o "%A"')
 set_alias("scancelall", 'squeue -h -u $USER -o "%A" | xargs scancel')
 

.modules.kuba/tools.lua

@@ -7,5 +7,6 @@ local loadscript = pathJoin(path, '.' .. myModuleName() .. '.sh');
 
 execute{cmd='source ' .. loadscript, modeA={"load"}}
 execute{cmd='unset -f npz_preview npz_previewi ' ..
+            'rsync_wrap rsync_wrap_huge selc selv cliipc clipv watch_modify pdftoclipboard gitgrepsed' ..
             'rsync_wrap rsync_wrap_huge selc selv cliipc clipv watch_modify' ..
             ';', modeA={"unload"}}

.ssh/config

@@ -15,15 +15,15 @@ Host aino
   User jakub
   Port 22209
 
-Host tahoe
+Host puffinus
-  HostName tahoe.fy.chalmers.se
+  HostName puffinus.fy.chalmers.se
   User jakub
   Port 22209
 
-Host geym
+Host sharknado
-  HostName geym.fy.chalmers.se
+  HostName 130.239.81.182
-  User jakub
+  User ubuntu
-  Port 22209
+  IdentityFile ~/.ssh/jupyterhub_rsa
 
 Host pi4
   HostName 192.168.0.200
@@ -48,11 +48,7 @@ Host vera2
   User fojt
 
 Host tetralith
-  Hostname tetralith1.nsc.liu.se
+  Hostname tetralith.nsc.liu.se
-  User x_jakfo
-
-Host tetralith2
-  Hostname tetralith2.nsc.liu.se
   User x_jakfo
 
 Host remote11
@@ -66,34 +62,7 @@ Host remote11
 Host dardel
   Hostname dardel.pdc.kth.se
   User fojt
-  GSSAPIAuthentication yes
+  IdentityFile ~/.ssh/id-ed25519-pdc
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host beskow
-  Hostname beskow.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host pdctransfer
-  Hostname t04n27.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host tegner
-  Hostname tegner.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
 
 Host *
     ForwardAgent no

.tmux.conf

@@ -11,9 +11,14 @@ set -g default-terminal "screen-256color"
 bind-key j command-prompt -p "join pane from:"  "join-pane -s '%%'"
 bind-key s command-prompt -p "send pane to:"  "join-pane -t '%%'"
 
-# ssh socket, important to create symlink in ~/.ssh/rc
+# Update the session environment upon attaching
-set -g update-environment -r
+set-option -g update-environment 'SSH_AUTH_SOCK SSH_CONNECTION DISPLAY'
-set-environment -g 'SSH_AUTH_SOCK' ~/.ssh/ssh_auth_sock
+set-hook -g client-attached 'run-shell /bin/update_display.sh'
+
+# Rename the session to the path
+set-option -g status-interval 5
+set-option -g automatic-rename on
+set-option -g automatic-rename-format '#{pane_current_path}'
 
 # Shorten delay for relaying Esc (to e.g. vim). Too short and PgUp will not work
 set -sg escape-time 20

.vimrc

@@ -2,46 +2,44 @@ let mapleader = ","
 set nocompatible              " be iMproved, required
 filetype off                  " required
 
-let vundle_dir="~/.vim/bundle/Vundle.vim"
+let plug_fpath="~/.vim/autoload/plug.vim"
-if filereadable(expand(vundle_dir) . "/README.md")
+if filereadable(expand(plug_fpath))
-    " set the runtime path to include Vundle and initialize
+    call plug#begin()
-    let &rtp .= "," . vundle_dir
-    call vundle#begin()
 
-    Plugin 'VundleVim/Vundle.vim' " let Vundle manage Vundle, required
+    Plug 'scrooloose/nerdtree'
-
+    Plug 'vim-scripts/c.vim'
-    Plugin 'scrooloose/nerdtree'
+    Plug 'jeetsukumaran/vim-buffergator'
-    Plugin 'c.vim'
+    Plug 'ericcurtin/CurtineIncSw.vim'
-    Plugin 'jeetsukumaran/vim-buffergator'
+    Plug 'tpope/vim-fugitive'
-    Plugin 'ericcurtin/CurtineIncSw.vim'
+    Plug 'tpope/vim-surround'
-    Plugin 'tpope/vim-fugitive'
+    Plug 'ctrlpvim/ctrlp.vim'
-    Plugin 'tpope/vim-surround'
+    Plug 'rhysd/vim-clang-format'
-    Plugin 'ctrlpvim/ctrlp.vim'
+    Plug 'godlygeek/tabular'
-    Plugin 'rhysd/vim-clang-format'
+    Plug 'airblade/vim-gitgutter'
-    Plugin 'godlygeek/tabular'
+    Plug 'jeetsukumaran/vim-pythonsense'
-    Plugin 'airblade/vim-gitgutter'
+    Plug 'easymotion/vim-easymotion'
-    Plugin 'jeetsukumaran/vim-pythonsense'
+    Plug 'cpiger/NeoDebug'
-    Plugin 'easymotion/vim-easymotion'
+    Plug 'ivan-krukov/vim-snakemake'
-    Plugin 'cpiger/NeoDebug'
+    Plug 'nvie/vim-flake8'
-    Plugin 'ivan-krukov/vim-snakemake'
+    Plug 'ludovicchabant/vim-gutentags'
-    Plugin 'nvie/vim-flake8'
+    Plug 'junegunn/vim-peekaboo'
-    Plugin 'ludovicchabant/vim-gutentags'
-    Plugin 'junegunn/vim-peekaboo'
     if has('python3') && empty($VIM_DISABLE_YCM)
-        Plugin 'ycm-core/YouCompleteMe'
+        Plug 'ycm-core/YouCompleteMe', { 'do': './install.py' }
     endif
-    Plugin 'dense-analysis/ale'
+    Plug 'dense-analysis/ale'
-    Plugin 'tpope/vim-unimpaired'
+    Plug 'tpope/vim-unimpaired'
-    Plugin 'JuliaEditorSupport/julia-vim'
+    Plug 'JuliaEditorSupport/julia-vim'
-    Plugin 'tell-k/vim-autopep8'
+    Plug 'tell-k/vim-autopep8'
-    Plugin 'jpalardy/vim-slime'
+    Plug 'tell-k/vim-autoflake'
-    Plugin 'preservim/tagbar'
+    Plug 'jpalardy/vim-slime'
+    Plug 'preservim/tagbar'
+    Plug 'wellle/context.vim'
 
-    call vundle#end()            " required
+    call plug#end()
 else
-    let vundle_repo="https://github.com/VundleVim/Vundle.vim.git"
+    let plug_url="https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim"
-    echo "Vundle not installed, type :CloneVundle to clone the vundle repo and install it"
+    echo "Plug not installed, type :CurlPlug to download and install plug"
-    command! CloneVundle execute "!git clone " . vundle_repo . " " .  vundle_dir | source $MYVIMRC | echo "Cloned Vundle. Do :PluginInstall"
+    command! CurlPlug execute "!curl -fLo " . plug_fpath . " --create-dirs " .  plug_url | source $MYVIMRC | echo "Curled Plug. Do :PlugInstall"
 endif
 
 set tabstop=4 " show existing tab with 4 spaces width
@@ -343,12 +341,16 @@ nmap <F2> :NERDTreeToggle<CR>
 nmap <F3> :NERDTreeFind<CR>
 map <F5> :call CurtineIncSw()<CR>
 
+let g:context_enabled = 0
+map <F6> :ContextToggle<CR>
+map cp :ContextPeek<CR>
+
 " Julialang
 let g:latex_to_unicode_auto = 1
 
 noremap <expr> <F7> LaTeXtoUnicode#Toggle()
 noremap! <expr> <F7> LaTeXtoUnicode#Toggle()
-autocmd FileType python noremap <buffer> <F8> :call Autopep8()<CR>
+autocmd FileType python noremap <buffer> :call Autoflake()<CR> :call Autopep8()<CR>
 
 let g:slime_target = "tmux"
 let g:slime_default_config = {"socket_name": "default", "target_pane": "{last}"}
@@ -395,3 +397,7 @@ nmap <Leader>p :set paste! <CR>
 map <Leader>n :noh<CR>
 vmap <Leader>T :'<,'> Tabularize /
 nnoremap <leader>c :execute "set colorcolumn=" . (&colorcolumn == "" ? "120" : "")<CR>
+
+" Insert "Embed IPython" command
+:command InsIPython :normal oimport IPython<CR>IPython.embed()<ESC><up>^
+nmap <Leader>i :InsIPython <CR>